The San Jose Museum is used for a number of purposes now. The mission has been turned into a historical museum to showcase the founding of the mission and the American West.
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The church on the mission is used for weddings and baptisms and hosts daily mass. Las Posadas is also annually celebrated at the mission. A religious and social celebration that takes place for nine nights, from December 16th to 24th. Las Posadas commemorates Joseph and Mary's journey to Bethlehem and their search for shelter prior to the birth of Christ.

The mission also host a number of lacal concerts including: The St. Innocent Orthodox Church choir , The Masterworks Concert, The California State University East Bay choral performance, and The San Francisco Bay Area Chamber performance